Research workbench
cryoEM structure of particulate methane monooxygenase associated with Cu(I)
Analyse cryoEM structure of particulate methane monooxygenase associated with Cu(I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EV9
- Type
- protein
- Length
- 2,142 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
- Molecule
- Particulate methane monooxygenase alpha subunit; Particulate methane monooxygenase beta…
- EC
- 1.14.18.3, 1.14.13.25
- UniProt
- G1UBD1, Q607G3, Q603F1
- Ligands
- CU1
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · resolution 2.6 · 3 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Particulate methane monooxygenase alpha subunit (EC 1.14.18.3) | protein | 382 | 20% helix, 38% strand | G1UBD1 |
| B, F, J | Particulate methane monooxygenase beta subunit (EC 1.14.18.3) | protein | 220 | 72% helix, 4% strand | Q607G3 |
| C, G, K | Ammonia monooxygenase/methane monooxygenase, subunit C family protein (EC 1.14.13.25) | protein | 112 | 61% helix, 1% strand | Q603F1 |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 24 copies · chains A, B, C, E, F, G, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.73 | 0.78 | 78 | empty |
| 2 | 836 | 0.72 | 0.77 | 82 | empty |
| 3 | 754 | 0.72 | 0.78 | 77 | empty |
| 4 | 301 | 0.64 | 0.80 | 30 | empty |
| 5 | 331 | 0.64 | 0.79 | 30 | empty |
Interfaces
18 interfaces between chains.
- I–J · 3807 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3805 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 3802 Ų buried · 41 hydrogen bonds · protein-protein
- J–K · 2173 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 2171 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7EV9 · Cryoem structure of particulate methane monooxygenase associated with CU(I) · the same entry in another collection · chain K against K, TM-score 1.00
- Q607G3 · AlphaFold monomer V2.0 prediction for particulate methane monooxygenase beta subunit… · a predicted model of the same protein · chain B against A, TM-score 0.99
- G1UBD1 · AlphaFold monomer V2.0 prediction for particulate methane monooxygenase alpha subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt G1UBD1
- Every structure of UniProt Q607G3
- Every structure of UniProt Q603F1
- Elsewhere: RCSB PDB 7EV9 · PDBe 7EV9 · UniProt G1UBD1 · UniProt Q607G3 · UniProt Q603F1
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